Hell to the yeah! Imagine some kind of dark plot I guess where the pokemon got possessed or something or just go crazy trying to take over the world from their masters idk hahaha.

Have you watched any of the pokemon movies?

One of the movie's plot is similar to that. Apparently Mew 2 is a genetically cloned/improved version of what's believed to be the strongest pokemon "Mew". Mew 2's master is the boss of Team Rocket. In the movie Mew 2 rebelled against his master. Ash convinced Mew 2 to stop being a bad guy. End of story